MolNFT v1 · #134358 · protein
Crystal structure of the putative periplasmic solute-binding protein from campylobacter jejuni
5T1P · ABC transporter, periplasmic substrate-binding protein: “Crystal structure of the putative periplasmic solute-binding protein from campylobacter jejuni”. X-ray diffraction, 1 ligand (GPE), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 5T1P
- Type
- protein
- Length
- 2,612 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, periplasmic substrate-binding protein
- UniProt
- A0A0W8LFT3
- Ligands
- GPE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, periplasmic substrate-binding protein | protein | 327 | 45% helix, 19% strand | A0A0W8LFT3 |
| B, E, G | ABC transporter, periplasmic substrate-binding protein | protein | 326 | 45% helix, 19% strand | A0A0W8LFT3 |
| C | ABC transporter, periplasmic substrate-binding protein | protein | 326 | 44% helix, 18% strand | A0A0W8LFT3 |
| D | ABC transporter, periplasmic substrate-binding protein | protein | 328 | 46% helix, 19% strand | A0A0W8LFT3 |
| F | ABC transporter, periplasmic substrate-binding protein | protein | 327 | 45% helix, 19% strand | A0A0W8LFT3 |
| H | ABC transporter, periplasmic substrate-binding protein | protein | 326 | 45% helix, 18% strand | A0A0W8LFT3 |
Ligands and binding sites
- GPE · L-alpha-glycerophosphorylethanolamine · ligand · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, D, E, F, H
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains E, G
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.84 | 0.85 | 96 | PEG |
| 2 | 1047 | 0.84 | 0.85 | 101 | PEG |
| 3 | 1038 | 0.76 | 0.78 | 113 | GPE |
| 4 | 406 | 0.68 | 0.81 | 61 | GPE |
| 5 | 519 | 0.66 | 0.77 | 45 | empty |
Interfaces
12 interfaces between chains.
- A–H · 940 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 912 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 783 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 759 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 332 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0W8LFT3
- Elsewhere: RCSB PDB 5T1P · PDBe 5T1P · UniProt A0A0W8LFT3
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